Aligning Scanned Images

I am scanning a series of images using a scanner with an automatic feeder.
I am scanning a series of drawings , intended for animation, and the top of the page has 3 holes made for the animation peg bar, which appear as gray shapes after the scan (a long hole, a circle, and a long hole).
I want to automatically align these drawings so that all these holes are exactly in the same spot.

The problem is, that I can't define a specific area to align by, and so I don't get a precise result.. is there a way to align specifically by the peg holes?
Maybe not in photoshop, but by using some plug in ?

Sometimes there is no easy solution. I would drag each layer over the other into one file, use on layer as your master guide, reduce opacity of layers above this so you can see your master below, then rotate your image to match.

There is a way of doing it using a free program called scan fix. You will probably have to rescan your images so that the holes will appear black. I used black tape on the scanner pad, but you can use a washable marker too.